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Coexpression cluster:C747: Difference between revisions

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{{Coexpression_clusters
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phase!6.90478736690457e-08!11065;83461;5347;332;1164$GO:0022403!cell cycle phase!8.83920725918899e-08!11065;83461;5347;332;1164$GO:0022402!cell cycle process!8.25432434157677e-07!11065;83461;5347;332;1164$GO:0007067!mitosis!1.31800666603262e-06!11065;83461;5347;332$GO:0000087!M phase of mitotic cell cycle!1.31800666603262e-06!11065;83461;5347;332$GO:0051301!cell division!1.31800666603262e-06!11065;83461;332;1164$GO:0007049!cell cycle!1.54018451911913e-06!11065;83461;5347;332;1164$GO:0000278!mitotic cell cycle!3.10586241182863e-06!11065;83461;5347;332$GO:0031536!positive regulation of exit from mitosis!3.50012641760176e-06!11065;332$GO:0010458!exit from mitosis!3.72023214421962e-05!11065;332$GO:0007096!regulation of exit from mitosis!3.72023214421962e-05!11065;332$GO:0007051!spindle organization and biogenesis!7.47271452394409e-05!11065;1164$GO:0000074!regulation of progression through cell cycle!0.000329835940259241!11065;332;1164$GO:0051726!regulation of cell cycle!0.000329835940259241!11065;332;1164$GO:0007088!regulation of mitosis!0.000770058464162874!11065;332$GO:0000226!microtubule cytoskeleton organization and biogenesis!0.00167727124825463!11065;1164$GO:0031021!interphase microtubule organizing center!0.00209861408357055!332$GO:0048015!phosphoinositide-mediated signaling!0.00225905088143288!11065;1164$GO:0005813!centrosome!0.00225905088143288!5347;332$GO:0005815!microtubule organizing center!0.00278551449326256!5347;332$GO:0008054!cyclin catabolic process!0.00339750608701829!11065$GO:0031503!protein complex localization!0.00486425299265298!332$GO:0045931!positive regulation of progression through mitotic cell cycle!0.00766592103107661!332$GO:0019932!second-messenger-mediated signaling!0.00766592103107661!11065;1164$GO:0050000!chromosome localization!0.00792518087701449!332$GO:0043027!caspase inhibitor activity!0.00792518087701449!332$GO:0051303!establishment of chromosome localization!0.00792518087701449!332$GO:0031577!spindle checkpoint!0.00844579235707201!332$GO:0005814!centriole!0.00844579235707201!332$GO:0007017!microtubule-based process!0.00844579235707201!11065;1164$GO:0030496!midbody!0.00891451629983814!332$GO:0005881!cytoplasmic microtubule!0.00891451629983814!332$GO:0043154!negative regulation of caspase activity!0.00972421121857813!332$GO:0016538!cyclin-dependent protein kinase regulator activity!0.0115338861723623!1164$GO:0000086!G2/M transition of mitotic cell cycle!0.0173081643590862!332$GO:0005876!spindle microtubule!0.0178159169112155!332$GO:0015630!microtubule cytoskeleton!0.0181776697464586!5347;332$GO:0043028!caspase regulator activity!0.0193994720605775!332$GO:0006512!ubiquitin cycle!0.0193994720605775!11065;83461$GO:0043161!proteasomal ubiquitin-dependent protein catabolic process!0.0195054927304112!11065$GO:0044450!microtubule organizing center part!0.0195054927304112!332$GO:0051656!establishment of organelle localization!0.0195054927304112!332$GO:0045787!positive regulation of progression through cell cycle!0.0198787562119038!332$GO:0050790!regulation of catalytic activity!0.0207930693452798!332;1164$GO:0043687!post-translational protein modification!0.0219524760693981!11065;83461;5347$GO:0065009!regulation of a molecular function!0.0234910667351854!332;1164$GO:0007346!regulation of progression through mitotic cell cycle!0.0234910667351854!332$GO:0007010!cytoskeleton organization and biogenesis!0.0234910667351854!11065;1164$GO:0051640!organelle localization!0.0234910667351854!332$GO:0007127!meiosis I!0.0234910667351854!1164$GO:0000910!cytokinesis!0.023726604291929!332$GO:0008283!cell proliferation!0.026393228548436!5347;1164$GO:0004869!cysteine protease inhibitor activity!0.0275176371779979!332$GO:0006464!protein modification process!0.031106816416925!11065;83461;5347$GO:0000079!regulation of cyclin-dependent protein kinase activity!0.031106816416925!1164$GO:0008017!microtubule binding!0.031106816416925!332$GO:0050794!regulation of cellular process!0.0316698104268787!11065;332;2305;1164$GO:0043412!biopolymer modification!0.0326941435235869!11065;83461;5347$GO:0000075!cell cycle checkpoint!0.0337256129752269!332$GO:0044430!cytoskeletal part!0.0342664867856905!5347;332$GO:0043281!regulation of caspase activity!0.0349395606960469!332$GO:0050789!regulation of biological process!0.0376828890740395!11065;332;2305;1164$GO:0015631!tubulin binding!0.0376828890740395!332$GO:0051327!M phase of meiotic cell cycle!0.0376828890740395!1164$GO:0007126!meiosis!0.0376828890740395!1164$GO:0051321!meiotic cell cycle!0.0381820259946129!1164$GO:0016567!protein ubiquitination!0.0386659523883696!11065$GO:0000775!chromosome, pericentric region!0.0395291491514415!332$GO:0032446!protein modification by small protein conjugation!0.0395291491514415!11065$GO:0005819!spindle!0.0395291491514415!332$GO:0016043!cellular component organization and biogenesis!0.0407942602760004!11065;332;1164$GO:0051329!interphase of mitotic cell cycle!0.0418585026518499!332$GO:0051325!interphase!0.0436975580360055!332$GO:0065007!biological regulation!0.0447251946760065!11065;332;2305;1164$GO:0019887!protein kinase regulator activity!0.0489140954037165!1164$GO:0046982!protein heterodimerization activity!0.0489140954037165!332|id=C747|ontology_enrichment_celltype=CL:0000548!3.90e-26!679;CL:0000255!3.90e-26!679;CL:0000066!4.56e-23!253;CL:0002321!4.27e-16!250;CL:0000003!2.15e-14!722;CL:0000333!4.78e-09!41;CL:0000133!2.76e-08!59;CL:0000222!2.51e-07!121;CL:0000076!2.64e-07!63;CL:1000449!3.93e-07!15;CL:1000497!4.13e-07!17;CL:0002518!4.13e-07!17;CL:0000221!5.19e-07!72;CL:0000213!6.78e-07!58;CL:0000215!6.78e-07!58;CL:0000055!8.04e-07!106;CL:0002319!9.53e-07!25|ontology_enrichment_disease=DOID:162!8.91e-38!235;DOID:14566!7.43e-37!239;DOID:0050687!1.44e-18!143;DOID:0050686!4.43e-17!137;DOID:2531!7.70e-15!51;DOID:0060083!7.70e-15!51;DOID:305!1.26e-14!106;DOID:1240!6.23e-11!39;DOID:8692!1.21e-07!31|ontology_enrichment_uberon=UBERON:0004211!3.93e-07!15;UBERON:0009773!3.93e-07!15;UBERON:0001231!3.93e-07!15;UBERON:0001285!3.93e-07!15;UBERON:0007684!3.93e-07!15;UBERON:0004208!3.93e-07!15|pathway_enrichment=2.59719623007301e-05;0.00822012606818106;3;315;Cell Cycle, Mitotic (Reactome):REACT_152!3.12165196450452e-07;0.000197600569353136;4;346;{CDC2,351} (Static 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|full_id=C747_Mesenchymal_alveolar_Trabecular_Alveolar_carcinoid_Renal_chronic
|id=C747
}}

Latest revision as of 11:30, 17 September 2013


Full id: C747_Mesenchymal_alveolar_Trabecular_Alveolar_carcinoid_Renal_chronic



Phase1 CAGE Peaks

Hg19::chr12:2986206..2986258,-p2@FOXM1
Hg19::chr12:6960407..6960464,-p1@CDCA3
Hg19::chr16:23690138..23690158,+p3@PLK1
Hg19::chr16:23690160..23690176,+p2@PLK1
Hg19::chr16:23690184..23690267,+p1@PLK1
Hg19::chr17:76210318..76210366,+p1@BIRC5
Hg19::chr17:76210367..76210385,+p2@BIRC5
Hg19::chr17:76220151..76220166,+p@chr17:76220151..76220166
+
Hg19::chr20:44441304..44441319,+p2@UBE2C
Hg19::chr3:52188397..52188450,-p1@POC1A
Hg19::chr9:91926103..91926119,+p1@CKS2


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

p.valueFDRnGenesnPathwayName
2.59719623007301e-050.008220126068181063315Cell Cycle, Mitotic (Reactome):REACT_152
3.12165196450452e-070.0001976005693531364346{CDC2,351} (Static Module):NA



Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

GO IDGO nameFDR corrected p-value
GO:0000279M phase6.90478736690457e-08
GO:0022403cell cycle phase8.83920725918899e-08
GO:0022402cell cycle process8.25432434157677e-07
GO:0007067mitosis1.31800666603262e-06
GO:0000087M phase of mitotic cell cycle1.31800666603262e-06
GO:0051301cell division1.31800666603262e-06
GO:0007049cell cycle1.54018451911913e-06
GO:0000278mitotic cell cycle3.10586241182863e-06
GO:0031536positive regulation of exit from mitosis3.50012641760176e-06
GO:0010458exit from mitosis3.72023214421962e-05
GO:0007096regulation of exit from mitosis3.72023214421962e-05
GO:0007051spindle organization and biogenesis7.47271452394409e-05
GO:0000074regulation of progression through cell cycle0.000329835940259241
GO:0051726regulation of cell cycle0.000329835940259241
GO:0007088regulation of mitosis0.000770058464162874
GO:0000226microtubule cytoskeleton organization and biogenesis0.00167727124825463
GO:0031021interphase microtubule organizing center0.00209861408357055
GO:0048015phosphoinositide-mediated signaling0.00225905088143288
GO:0005813centrosome0.00225905088143288
GO:0005815microtubule organizing center0.00278551449326256
GO:0008054cyclin catabolic process0.00339750608701829
GO:0031503protein complex localization0.00486425299265298
GO:0045931positive regulation of progression through mitotic cell cycle0.00766592103107661
GO:0019932second-messenger-mediated signaling0.00766592103107661
GO:0050000chromosome localization0.00792518087701449
GO:0043027caspase inhibitor activity0.00792518087701449
GO:0051303establishment of chromosome localization0.00792518087701449
GO:0031577spindle checkpoint0.00844579235707201
GO:0005814centriole0.00844579235707201
GO:0007017microtubule-based process0.00844579235707201
GO:0030496midbody0.00891451629983814
GO:0005881cytoplasmic microtubule0.00891451629983814
GO:0043154negative regulation of caspase activity0.00972421121857813
GO:0016538cyclin-dependent protein kinase regulator activity0.0115338861723623
GO:0000086G2/M transition of mitotic cell cycle0.0173081643590862
GO:0005876spindle microtubule0.0178159169112155
GO:0015630microtubule cytoskeleton0.0181776697464586
GO:0043028caspase regulator activity0.0193994720605775
GO:0006512ubiquitin cycle0.0193994720605775
GO:0043161proteasomal ubiquitin-dependent protein catabolic process0.0195054927304112
GO:0044450microtubule organizing center part0.0195054927304112
GO:0051656establishment of organelle localization0.0195054927304112
GO:0045787positive regulation of progression through cell cycle0.0198787562119038
GO:0050790regulation of catalytic activity0.0207930693452798
GO:0043687post-translational protein modification0.0219524760693981
GO:0065009regulation of a molecular function0.0234910667351854
GO:0007346regulation of progression through mitotic cell cycle0.0234910667351854
GO:0007010cytoskeleton organization and biogenesis0.0234910667351854
GO:0051640organelle localization0.0234910667351854
GO:0007127meiosis I0.0234910667351854
GO:0000910cytokinesis0.023726604291929
GO:0008283cell proliferation0.026393228548436
GO:0004869cysteine protease inhibitor activity0.0275176371779979
GO:0006464protein modification process0.031106816416925
GO:0000079regulation of cyclin-dependent protein kinase activity0.031106816416925
GO:0008017microtubule binding0.031106816416925
GO:0050794regulation of cellular process0.0316698104268787
GO:0043412biopolymer modification0.0326941435235869
GO:0000075cell cycle checkpoint0.0337256129752269
GO:0044430cytoskeletal part0.0342664867856905
GO:0043281regulation of caspase activity0.0349395606960469
GO:0050789regulation of biological process0.0376828890740395
GO:0015631tubulin binding0.0376828890740395
GO:0051327M phase of meiotic cell cycle0.0376828890740395
GO:0007126meiosis0.0376828890740395
GO:0051321meiotic cell cycle0.0381820259946129
GO:0016567protein ubiquitination0.0386659523883696
GO:0000775chromosome, pericentric region0.0395291491514415
GO:0032446protein modification by small protein conjugation0.0395291491514415
GO:0005819spindle0.0395291491514415
GO:0016043cellular component organization and biogenesis0.0407942602760004
GO:0051329interphase of mitotic cell cycle0.0418585026518499
GO:0051325interphase0.0436975580360055
GO:0065007biological regulation0.0447251946760065
GO:0019887protein kinase regulator activity0.0489140954037165
GO:0046982protein heterodimerization activity0.0489140954037165



Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br>disease_data<br>

Cell Type
Ontology termp-valuen
animal cell3.90e-26679
eukaryotic cell3.90e-26679
epithelial cell4.56e-23253
embryonic cell4.27e-16250
native cell2.15e-14722
migratory neural crest cell4.78e-0941
neurectodermal cell2.76e-0859
mesodermal cell2.51e-07121
squamous epithelial cell2.64e-0763
epithelial cell of nephron3.93e-0715
kidney cell4.13e-0717
kidney epithelial cell4.13e-0717
ectodermal cell5.19e-0772
lining cell6.78e-0758
barrier cell6.78e-0758
non-terminally differentiated cell8.04e-07106
neural cell9.53e-0725
Uber Anatomy
Ontology termp-valuen
nephron epithelium3.93e-0715
renal tubule3.93e-0715
nephron tubule3.93e-0715
nephron3.93e-0715
uriniferous tubule3.93e-0715
nephrogenic mesenchyme3.93e-0715
Disease
Ontology termp-valuen
cancer8.91e-38235
disease of cellular proliferation7.43e-37239
cell type cancer1.44e-18143
organ system cancer4.43e-17137
hematologic cancer7.70e-1551
immune system cancer7.70e-1551
carcinoma1.26e-14106
leukemia6.23e-1139
myeloid leukemia1.21e-0731


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.12.25715
MA0004.11.64978
MA0006.10.605586
MA0007.10.885261
MA0009.10.79061
MA0014.12.1035
MA0017.10.24363
MA0019.10.486183
MA0024.10.688373
MA0025.12.12648
MA0027.12.39404
MA0028.10.224112
MA0029.10.707146
MA0030.10.696006
MA0031.10.633489
MA0038.11.97347
MA0040.10.712837
MA0041.10.366339
MA0042.10.337481
MA0043.10.790919
MA0046.10.779945
MA0048.11.12059
MA0050.11.61016
MA0051.10.439895
MA0052.10.716602
MA0055.10.736537
MA0056.10
MA0057.10.0465155
MA0058.12.8909
MA0059.11.34253
MA0060.16.47493
MA0061.10.330174
MA0063.10
MA0066.10.444231
MA0067.11.1037
MA0068.10.0758327
MA0069.10.776171
MA0070.10.765217
MA0071.10.40788
MA0072.10.760818
MA0073.10.00132306
MA0074.11.11883
MA0076.10.278993
MA0077.10.753278
MA0078.10.533387
MA0081.10.26424
MA0083.10.79797
MA0084.11.28962
MA0087.10.758426
MA0088.12.47064
MA0089.10
MA0090.10.792817
MA0091.10.351901
MA0092.10.318032
MA0093.12.53685
MA0095.10
MA0098.10
MA0100.12.01706
MA0101.10.617985
MA0103.10.203171
MA0105.10.360248
MA0106.10.482519
MA0107.10.156959
MA0108.20.630531
MA0109.10
MA0111.10.303543
MA0113.10.498009
MA0114.10.153042
MA0115.11.02805
MA0116.10.935607
MA0117.10.827487
MA0119.10.698186
MA0122.10.852927
MA0124.10.98702
MA0125.10.904129
MA0130.10
MA0131.12.32762
MA0132.10
MA0133.10
MA0135.10.820382
MA0136.10.450422
MA0139.10.637178
MA0140.11.04551
MA0141.10.2626
MA0142.10.602852
MA0143.10.498176
MA0144.12.00452
MA0145.11.62175
MA0146.10.700193
MA0147.11.51125
MA0148.10.372124
MA0149.10.396509
MA0062.20.320507
MA0035.20.404774
MA0039.20.556508
MA0138.21.323
MA0002.20.111226
MA0137.21.21272
MA0104.22.45237
MA0047.20.47109
MA0112.20.106997
MA0065.20.11899
MA0150.10.286461
MA0151.10
MA0152.10.411494
MA0153.10.887528
MA0154.10.353037
MA0155.10.462858
MA0156.10.231442
MA0157.10.576556
MA0158.10
MA0159.10.489747
MA0160.10.386031
MA0161.10
MA0162.10.178494
MA0163.10.585549
MA0164.10.509774
MA0080.20.21336
MA0018.20.483823
MA0099.20.411824
MA0079.20.239
MA0102.21.32663
MA0258.10.135061
MA0259.11.54967
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
ATF3#46736.126320325275110.01111623399164760.0408820466882767
BCLAF1#977435.905267530033230.01228645577323260.0445303010306995
CHD2#110676.582559985347091.82852745688608e-050.000416055727820751
E2F1#1869104.461262922617571.10540139252827e-064.58123079501033e-05
E2F4#18741011.51641846844049.56616236582045e-111.03854514690636e-08
E2F6#187694.10494559866151.83835844928222e-050.000418201520550175
EBF1#187975.667751629634824.91015352587259e-050.000852129485025934
ELF1#199783.096798515496390.0007580113527617290.00595770226302545
ETS1#211376.191029677765122.74425924207753e-050.000583722384894777
FOSL2#235546.156436583476980.002867376563988960.015536494991774
HDAC2#306667.317611038159785.69712326977083e-050.000950482199954626
HEY1#23462103.672828221005197.3527784911531e-060.000211140179498911
HNF4A#3172612.61761292524752.49318000901648e-068.78492668561648e-05
HNF4G#317437.841842507212760.005623677651235930.0254211941749234
IRF1#365953.471438069801770.008947162075865850.0339324809369364
IRF3#3661312.81325969404260.001398658583494010.00909951434632351
MAX#414995.279363598278552.09889244785612e-067.65652212230686e-05
MXI1#460187.24477936637041.28440155682788e-065.13166083372406e-05
MYC#460994.272776076771331.30375226575527e-050.000318732637835241
NFYA#4800610.05031674536219.29686132166058e-060.000247566267101711
NFYB#4801710.66532297952327.15961572771292e-073.20369797337879e-05
NRF1#489944.440101617349420.009277033757250970.0350460872666402
PBX3#509059.961142130338247.24136591048148e-050.00113863446902255
POLR2A#5430101.952230160507340.00304073181841430.0161342778226577
POU2F2#545286.62263567835822.56270583551105e-069.01166446986324e-05
SIN3A#25942104.91716793346834.26535327044908e-072.04907649591735e-05
SP1#6667105.180346707400822.55812246304286e-071.32919279561061e-05
TAF1#6872103.039132987041174.59104772732301e-050.00080707697962277
TAF7#687966.236219675413040.0001401960028212370.00182886964010082
TBP#6908103.369791533723991.6942293653553e-050.000390001368058942
THAP1#5514538.555221255323090.0044077462426430.0208828075592176
USF1#739195.204863044988332.37429471822852e-068.41143032825877e-05
USF2#739267.086653119128876.8302134157013e-050.00109040149636568
ZNF143#770267.36411448303345.49636173278436e-050.000930514707424649



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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